landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Bug fixes

Browse Source
This commit is contained in:
lwark
2025-08-13 09:45:51 -05:00
parent 6380f1e2a9
commit 6f58030e75
11 changed files with 110 additions and 50 deletions
Download Patch File Download Diff File Expand all files Collapse all files

31
src/submissions/backend/validators/pydant.py
View File

@@ -25,9 +25,13 @@ logger = logging.getLogger(f"submission.{__name__}")
class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
_sql_object: ClassVar = None
# _sql_object: ClassVar = None
key_value_order: ClassVar = []
@classproperty
def _sql_object(cls):
return getattr(models, cls.__name__.replace("Pyd", ""))
@model_validator(mode="before")
@classmethod
def prevalidate(cls, data):
@@ -36,7 +40,7 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
try:
items = data.items()
except AttributeError as e:
logger.error(f"Could not prevalidate {cls.__name__} due to {e}")
logger.error(f"Could not prevalidate {cls.__name__} due to {e} for {pformat(data)}")
return data
for key, value in items:
new_key = key.replace("_", "")
@@ -67,7 +71,8 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
def __init__(self, **data):
# NOTE: Grab the sql model for validation purposes.
self.__class__._sql_object = getattr(models, self.__class__.__name__.replace("Pyd", ""))
# self.__class__._sql_object = getattr(models, self.__class__.__name__.replace("Pyd", ""))
logger.debug(f"Initial data: {data}")
super().__init__(**data)
def filter_field(self, key: str) -> Any:
@@ -398,14 +403,17 @@ class PydEquipment(PydBaseClass):
# if isinstance(value, dict):
# value = value['processes']
if isinstance(value, GeneratorType):
value = [item.name for item in value]
value = [item for item in value]
value = convert_nans_to_nones(value)
if not value:
value = ['']
# logger.debug(value)
try:
# value = [item.strip() for item in value]
value = next((PydProcess(**process.details_dict()) for process in value))
d = next((process for process in value), None)
logger.debug(f"Next process: {d.detail_dict()}")
value = PydProcess(d.details_dict())
# value = next((process.to_pydantic() for process in value))
except AttributeError:
pass
return value
@@ -1461,7 +1469,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
idx = 0
insertable = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
self.reagent.insert(idx, insertable)
# logger.debug(self.reagent)
logger.debug(self.reagent)
@classmethod
def update_new_reagents(cls, reagent: PydReagent):
@@ -1501,9 +1509,9 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
for reagent in self.reagent:
if not reagent.lot or reagent.name == "--New--":
continue
self.update_new_reagents(reagent)
# self.update_new_reagents(reagent)
# NOTE: reset reagent associations.
sql.procedurereagentassociation = []
# sql.procedurereagentassociation = []
for reagent in self.reagent:
if isinstance(reagent, dict):
reagent = PydReagent(**reagent)
@@ -1542,12 +1550,13 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
logger.debug(f"sample {sample_sql} not found in {sql.run.sample}")
run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row,
column=sample.column)
else:
logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
# else:
# logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
if sample_sql not in sql.sample:
proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql,
row=sample.row, column=sample.column,
procedure_rank=sample.procedure_rank)
sys.exit(pformat(self.equipment))
for equipment in self.equipment:
equip = Equipment.query(name=equipment.name)
if equip not in sql.equipment:
@@ -1555,8 +1564,6 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
equipmentrole=equip.equipmentrole[0])
process = equipment.process.to_sql()
equip_assoc.process = process
# logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
logger.debug(pformat(sql.__dict__))
return sql, None